My names Patrick and I'm a simaholic! haha... had to start it off that way, anyway.....
I have always used a 3 man rotation with 4-6 relief pitchers(50 IP min., plus milacki occasionally) that has worked well in every update. Granted, sometimes I will go with a weaker 3-man rotation for a stronger hitting lineup, and vice versa, but ALL of my teams have competed, and competed well. I don't have time to really figure out the fatigue system in detail, but I have never had any problems with it with this rotation.
The fact is pitchers are going to underperform, even the best of the best, most of the time, dont even come close to matching their real stats due to all the great hitting teams out there. The key for me is finding above average starters for cheap $$/IP, spend minimum of $10 mil on relief pitching(getting great relief pitchers is key in winning games late. So many owners use their mop up pitchers innefectively, and it has helped me win countless games over the years).
I think the key to beating the fatigue system is hitting. Hitting obviously helps win games(keeping them 9 innings) and preventing those 18 inning games that ruin your staff. Granted, you could say the same about pitching, but hitters are more reliable and seem to come much closer to their real #s than pitchers in the sim(as always, there are some exceptions.) Finding cheap, low PA (min 520), good hitters like the cedeno's, figgin's, '22 ruth, '23 williams, etc. are always good ways to go. Your going to be giving up defense and PA's but the $$ ur saving can go towards other more powerful hitters, or towards ur staff. Also, to be honest, I don't think defense has THAT much of an effect on the sim as a lot of you out there might think. I usually draft jsut average defense and I have never had a problem, but that can be debatable on another thread. You can also go with the strategy of not drafting a 1B and rotate ur AAA without taking a hit on defense(you could put an F/F OF at 1b and get minimal errors, this strategy is risky, but pays huge dividends if u catch some good AAA hitters).
EVERY team I have created using a variation of this strategy has at least made it to the playoffs, the better pitching teams ive had have won me two TOCs, but I havent had much success winning OL championshipss(which is all I play). I have two TOCs and one OL champ lol.
Haven't tried many other strategies bc im too scared my teams will flop! Maybe a few more TOCs and free teams and ill move away from the norm. Hope this info helps for the newer guys, im sure all u vets have heard this a million times, but figuring this out really helped me when I was new to the sim.